Beginning Perl Scripting
Simple scripts, Expressions, Operators, Statements, Variables
Simon Prochnik & Lincoln Stein
Suggested Reading
Learning Perl (6th ed.): Chap. 2, 3, 12, Unix & Perl to the Rescue (1st ed.): Chap. 4 Chapters 1, 2 & 5 of Learning Perl.
Lecture Notes
1. What is Perl? 2. Some simple Perl scripts 3. Mechanics of creating a Perl script 4. Statements 5. Literals 6. Operators 7. Functions 8. Variables 9. Processing the Command Line
Problems
What is Perl?
Perl is a Programming Language
Written by Larry Wall in late 80's to process mail on Unix systems and since extended by a huge cast of characters. The name is said to stand for:
1. Pathologically Eclectic Rubbish Lister 2. Practical Extraction and Report Language
Perl Properties
1. Interpreted Language 2. "Object-Oriented" 3. Cross-platform 4. Forgiving 5. Great for text 6. Extensible, rich set of libraries 7. Popular for web pages 8. Extremely popular for bioinformatics
Other Languages Used in Bioinformatics
1 of 20 C, C++ Compiled languages, hence very fast. Used for computation (BLAST, FASTA, Phred, Phrap, ClustalW) Not very forgiving.
Java Interpreted, fully object-oriented language. Built into web browsers. Supposed to be cross-platform, getting better.
Python , Ruby Interpreted, fully object-oriented language. Rich set of libraries. Elegant syntax. Smaller user community than Java or Perl.
Some Simple Scripts
Here are some simple scripts to illustrate the "look" of a Perl program.
Print a Message to the Terminal
Code:
#!/usr/bin/perl # file: message.pl use strict; use warnings; print "When that Aprill with his shoures soote\n"; print "The droghte of March ath perced to the roote,\n"; print "And bathed every veyne in swich licour\n"; print "Of which vertu engendered is the flour...\n";
Output:
(~) 50% perl message.pl When that Aprill with his shoures soote The droghte of March ath perced to the roote, And bathed every veyne in swich licour Of which vertu engendered is the flour...
Do Some Math
Code:
#!/usr/bin/perl # file: math.pl use strict; use warnings; print "2 + 2 =", 2+2, "\n"; print "log(1e23)= ", log(1e23), "\n"; print "2 * sin(3.1414)= ", 2 * sin(3.1414), "\n";
2 of 20 Output:
(~) 51% perl math.pl 2 + 2 =4 log(1e23)= 52.9594571388631 2 * sin(3.1414)= 0.000385307177203065
Run a System Command
Code:
#!/usr/bin/perl # file: system.pl use strict; use warnings; system "ls";
Output:
(~/docs/grad_course/perl) 52% perl system.pl index.html math.pl~ problem_set.html~ what_is_perl.html index.html~ message.pl simple.html what_is_perl.html~ math.pl problem_set.html simple.html~
Return the Time of Day
Code:
#!/usr/bin/perl # file: time.pl use strict; use warnings; $time = localtime; print "The time is now $time\n";
Output:
(~) 53% perl time.pl The time is now Thu Sep 16 17:30:02 1999
Mechanics of Writing Perl Scripts
Some hints to help you get going.
Creating the Script
A Perl script is just a text file. Use any text (programmer's) editor. Don't use word processors like Word.
By convention, Perl script files end with the extension .pl.
3 of 20 I suggest Emacs, because it is already installed on almost all Unix machines, but there are many good options: vi, vim, Textwrangler, eclipse
The Emacs text editor has a Perl mode that will auto-format your Perl scripts and highlight keywords. Perl mode will be activated automatically if you end the script name with .pl.
GUI-based script writing tools (Aquamacs, xemacs, Textwrangler, Eclipse) are easier to use, but you may have to install them yourself.
Let's write a simple perl script. It'll be a simple text file called time.pl and will contain the lines above.
Let's try doing this in emacs
Emacs Essentials
A GUI version is simpler to use e.g. Aquamacs, run it by adding the icon for the application to your Dock then clicking on the icon. You can also run emacs in a Terminal window. Emacs will be installed on almost every Unix system you encounter.
(~) 50% emacs
The same shortcuts you can use on the command line work in Emacs e.g. control-a (^a)
move cursor to beginning of line etc
The most important Emacs-specific commands control-x control-f (^x ^f)
open a file control-x control-w (^x ^w)
save as... control-x control-c (^x ^c)
quit control-g (^g)
cancel command shift-control-_ (^_)
Undo typing control-h ?(^h ?)
Help!! option-; (M;)
Add comment option-/ (M/)
Variable/subroutine name auto-completion (cycles through options)
Running the Script
Don't forget to save any changes in your script before running it. The filled red circle at the top left of the emacs GUI window has a dot in it if there are unsaved changes.
Option 1 (quick, not used much) Run the perl program from the command line, giving it the name of the script file to run.
(~) 50% perl time.pl The time is now Thu Sep 16 18:09:28 1999
4 of 20 Option 2 (as shown in examples above) Put the magic comment
#!/usr/bin/perl
at the top of your script.
It's really easy to make a mistake with this complicated line and this causes confusing errors (see below). Double check, or copy from a friend who has it working.
And always add
use strict; use warnings;
to the top of your script like in the example below
#!/usr/bin/perl # file: time.pl use strict; use warnings; $time = localtime; print "The time is now $time\n";
Now make the script executable with chmod +x time.pl:
(~) 51% chmod +x time.pl
Run the script as if it were a command:
(~) 52% ./time.pl The time is now Thu Sep 16 18:12:13 1999
Note that you have to type "./time.pl" rather than "time.pl" because, by default, bash does not search the current directory for commands to execute. To avoid this, you can add the current directory (".") to your search PATH environment variable. To do this, create a file in your home directory named .profile and enter the following line in it:
export PATH=$PATH:.
The next time you log in, your path will contain the current directory and you can type "time.pl" directly.
Common Errors
Plan out your script before you start coding. Write the code, then run it to see if it works. Every script goes through a few iterations before you get it right. Here are some common errors:
Syntax Errors
Code:
5 of 20
#!/usr/bin/perl # file: time.pl use strict; use warnings; time = localtime; print "The time is now $time\n";
Output:
(~) 53% time.pl Can't modify time in scalar assignment at time.pl line 3, near "localtime;" Execution of time.pl aborted due to compilation errors.
Runtime Errors
Code:
#!/usr/bin/perl # file: math.pl use strict; use warnings;
$six_of_one = 6; $half_dozen = 12/2; $result = $six_of_one/($half_dozen - $six_of_one); print "The result is $result\n";
Output:
(~) 54% math.pl Illegal division by zero at math.pl line 6.
Forgetting to Make the Script Executable
(~) 55% test.pl test.pl: Permission denied.
Getting the Path to Perl Wrong on the #! line
Code:
#!/usr/local/bin/pearl # file: time.pl use strict; use warnings; $time = localtime; print "The time is now $time\n";
(~) 55% time.pl
6 of 20 time.pl: Command not found.
This gives a very confusing error message because the command that wasn't found is 'pearl' not time.pl
Useful Perl Command-Line Options
You can call Perl with a few command-line options to help catch errors:
-c Perform a syntax check, but don't run.
-w Turn on verbose warnings. Same as
use warnings;
-d Turn on the Perl debugger.
Usually you will invoke these from the command-line, as in perl -cw time.pl (syntax check time.pl with verbose warnings). You can also put them in the top line: #!/usr/bin/perl -w.
Perl Statements
A Perl script consists of a series of statements and comments. Each statement is a command that is recognized by the Perl interpreter and executed. Statements are terminated by the semicolon character (;). They are also usually separated by a newline character to enhance readability.
A comment begins with the # sign and can appear anywhere. Everything from the # to the end of the line is ignored by the Perl interpreter. Commonly used for human-readable notes. Use comments plentifully, especially at the beginning of a script to describe what it does, at the beginning of each section of your code and for any complex code.
Some Statements
$sum = 2 + 2; # this is a statement
$f =
$g = $f / $sum; # this is one statement, spread across 3 lines
The Perl interpreter will start at the top of the script and execute all the statements, in order from top to bottom, until it reaches the end of the script. This execution order can be modified by loops and control structures.
Blocks
It is common to group statements into blocks using curly braces. You can execute the entire block conditionally, or turn it into a subroutine that can be called from many different places.
Example blocks: { # block starts
7 of 20 my $EcoRI = 'GAATTC'; my $sequence =
my $sequence2 =
foreach $sequence (@sequences) { # another block print "sequence length = ",length($sequence),"\n"; }
Literals
A literal is a constant value that you embed directly in the program code. You can think of the value as being literally in the code. Perl supports both string literals and numeric literals. A string literal or a numeric literal is a scalar i.e. a single value.
Literals cannot be changed. If you want to change the value of some data, it needs to be a variable. Much, much more on this coming up, until you're really sick of the whole thing.
String Literals
String literals are enclosed by single quotes (') or double quotes ("):
'The quality of mercy is not strained.'; # a single-quoted string "The quality of mercy is not strained."; # a double-quoted string
The difference between single and double-quoted strings is that variables and certain special escape codes are interpolated into double quoted strings, but not in single-quoted ones. Here are some escape codes:
\n New line
\t Tab
\r Carriage return
\f Form feed
\a Ring bell
\040 Octal character (octal 040 is the space character)
\0x2a Hexadecimal character (hex 2A is the "*" character)
\cA Control character (This is the ^A character)
\u Uppercase next character
8 of 20 \l Lowercase next character
\U Uppercase everything until \E
\L Lowercase everything until \E
\Q Quote non-word characters until \E
\E End \U, \L or \Q operation
"Here goes\n\tnothing!"; # evaluates to: # Here goes # nothing!
'Here goes\n\tnothing!'; # evaluates to: # Here goes\n\tnothing!
"Here goes \unothing!"; # evaluates to: # Here goes Nothing!
"Here \Ugoes nothing\E"; # evaluates to: # Here GOES NOTHING!
"Alert! \a\a\a"; # evaluates to: # Alert! (ding! ding! ding!)
Putting backslashes in strings is a problem because they get interpreted as escape sequences. To inclue a literal backslash in a string, double it:
"My file is in C:\\Program Files\\Accessories\\wordpad.exe";
# evaluates to: C:\Program Files\Accessories\wordpad.exe
Put a backslash in front of a quote character in order to make the quote character part of the string:
"She cried \"Oh dear! The parakeet has flown the coop!\"";
# evaluates to: She cried "Oh dear! The parakeet has flown the coop!"
Numeric Literals
You can refer to numeric values using integers, floating point numbers, scientific notation, hexadecimal notation, and octal. With some help from the Math::Complex module, you can refer to complex numbers as well:
9 of 20 123; # an integer
1.23; # a floating point number
-1.23; # a negative floating point number
1_000_000; # you can use _ to improve readability
1.23E45; # scientific notation
0x7b; # hexadecimal notation (decimal 123)
0173; # octal notation (decimal 123)
use Math::Complex; # bring in the Math::Complex module
12+3*i; # complex number 12 + 3i
Backtick Strings
You can also enclose a string in backtics (`). This has the helpful property of executing whatever is inside the string as a Unix system command, and returning its output:
`ls -l`; # evaluates to a string containing the output of running the # ls -l command
Lists
The last type of literal that Perl recognizes is the list, which is multiple values strung together using the comma operator (,) and enclosed by parentheses. Lists are closely related to arrays, which we talk about later. Lists (and arrays) are composed from zero, one or more scalars, making an empty list, a list containing a single item or a more typical list containing many items, respectively.
('one', 'two', 'three', 1, 2, 3, 4.2); # this is 7-member list contains a mixure of strings, integers # and floats
Operators
Perl has numerous operators (over 50 of them!) that perform operations on string and numberic values. Some operators will be familiar from algebra (like "+", to add two numbers together), while others are more esoteric (like the "." string concatenation operator).
Numeric & String Operators
10 of 20 The "." operator acts on strings. The "!" operator acts on strings and numbers. The rest act on numbers. Operator Description Example Result . String concatenate 'Teddy' . 'Bear' Te d d y B e a r
= Assignment $a = 'Teddy' $a variable contains 'Teddy'
+ Addition 3+2 5
- Subtraction 3-2 1
- Negation -2 -2
! Not !1 0
* Multiplication 3*2 6
/ Division 3/2 1.5
% Modulus 3%2 1
** Exponentiation 3**2 9
>> Right bit shift 3>>2 0 (binary 11>>2=00)
<< Left bit shift 3<<2 12 (binary 11<<2=1100)
| Bitwise OR 3|2 3 (binary 11|10=11
& Bitwise AND 3&2 2 (binary 11&10=10
^ Bitwise XOR 3^2 1 (binary 11^10=01
Operator Precedence
When you have an expression that contains several operators, they are evaluated in an order determined by their precedence. The precedence of the mathematical operators follows the rules of arithmetic. Others follow a precedence that usually does what you think they should do. If uncertain, use parentheses to force precedence:
2+3*4; # evaluates to 14, multiplication has precedence over addition (2+3)*4; # evaluates to 20, parentheses force the precedence
Logical Operators
These operators compare strings or numbers, returning TRUE or FALSE:
Numeric Comparison String Comparison 3 == 2 equal to 'Teddy' eq 'Bear' equal to
3 != 2 not equal to 'Teddy' ne 'Bear' not equal to
3 < 2 less than 'Teddy' lt 'Bear' less than
3 > 2 greater than 'Teddy' gt 'Bear' greater than
11 of 20 3 <= 2 less or equal 'Teddy' le 'Bear' less than or equal
3 >= 2 greater than or equal 'Teddy' ge 'Bear' greater than or equal
3 <=> 2 compare 'Teddy' cmp 'Bear' compare
'Teddy' =~ /Bear/ pattern match
The <=> and cmp operators return:
-1 if the left side is less than the right side 0 if the left side equals the right side +1 if the left side is greater than the right side
File Operators
Perl has special file operators that can be used to query the file system. These operators generally return TRUE or FALSE.
Example:
print "Is a directory!\n" if -d '/usr/home'; print "File exists!\n" if -e '/usr/home/lstein/test.txt'; print "File is plain text!\n" if -T '/usr/home/lstein/test.txt';
There are many of these operators. Here are some of the most useful ones:
-e filename file exists
-r filename file is readable
-w filename file is writable
-x filename file is executable
-z filename file has zero size
-s filename file has nonzero size (returns size)
-d filename file is a directory
-T filename file is a text file
-B filename file is a binary file
-M filename age of file in days since script launched
-A filename same for access time
Functions
In addition to its operators, Perl has many functions. Functions have a human-readable name, such as print and take one or more arguments passed as a list. A function may return no value, a single value (AKA "scalar"), or a list (AKA "array"). You can enclose the argument list in parentheses, or leave the parentheses off.
12 of 20 A few examples:
# The function is print. Its argument is a string. # The effect is to print the string to the terminal. print "The rain in Spain falls mainly on the plain.\n";
# Same thing, with parentheses. print("The rain in Spain falls mainly on the plain.\n");
# You can pass a list to print. It will print each argument. # This prints out "The rain in Spain falls 6 times in the plain." print "The rain in Spain falls ",2*4-2," times in the plain.\n";
# Same thing, but with parentheses. print ("The rain in Spain falls ",2*4-2," times in the plain.\n");
# The length function calculates the length of a string, # yielding 45. length "The rain in Spain falls mainly on the plain.\n";
# The split function splits a string based on a delimiter pattern # yielding the list ('The','rain in Spain','falls mainly','on the plain.') split '/','The/rain in Spain/falls mainly/on the plain.';
Creating Your Own Functions
You can define your own functions or redefine the built-in ones using the sub function. This is described in more detail in the lesson on creating subroutines, which you'll be seeing soon..
Often Used Functions (alphabetic listing)
For specific information on a function, use perldoc -f function_name to get a concise summary.
abs absolute value
chdir change current directory
chmod change permissions of file/directory
chomp remove terminal newline from string variable
chop remove last character from string variable
chown change ownership of file/directory
close close a file handle
closedir close a directory handle
cos cosine
defined test whether variable is defined
delete delete a key from a hash
13 of 20 die exit with an error message each iterate through keys & values of a hash eof test a filehandle for end of file eval evaluate a string as a perl expression exec quit Perl and execute a system command exists test that a hash key exists exit exit from the Perl script glob expand a directory listing using shell wildcards gmtime current time in GMT grep filter an array for entries that meet a criterion index find location of a substring inside a larger string int throw away the fractional part of a floating point number join join an array together into a string keys return the keys of a hash kill send a signal to one or more processes last exit enclosing loop lc convert string to lowercase lcfirst lowercase first character of string length find length of string local temporarily replace the value of a global variable localtime return time in local timezone log natural logarithm m// pattern match operation map perform on operation on each member of array or list mkdir make a new directory my create a local variable next jump to the top of enclosing loop open open a file for reading or writing opendir open a directory for listing pack pack a list into a compact binary representation
14 of 20 package create a new namespace for a module pop pop the last item off the end of an array print print to terminal or a file printf formatted print to a terminal or file push push a value onto the end of an array q/STRING/ generalized single-quote operation qq/STRING/ generalized double-quote operation qx/STRING/ generalized backtick operation qw/STRING/ turn a space-delimited string of words into a list rand random number generator read read binary data from a file readdir read the contents of a directory readline read a line from a text file readlink determine the target of a symbolic link redo restart a loop from the top ref return the type of a variable reference rename rename or move a file require load functions defined in a library file return return a value from a user-defined subroutine reverse reverse a string or list rewinddir rewind a directory handle to the beginning rindex find a substring in a larger string, from right to left rmdir remove a directory s/// pattern substitution operation scalar force an expression to be treated as a scalar seek reposition a filehandle to an arbitrary point in a file select make a filehandle the default for output shift shift a value off the beginning of an array sin sine sleep put the script to sleep for a while
15 of 20 sort sort an array or list by user-specified criteria
splice insert/delete array items
split split a string into pieces according to a pattern
sprintf formatted string creation
sqrt square root
stat get information about a file
sub define a subroutine
substr extract a substring from a string
symlink create a symbolic link
system execute an operating system command, then return to Perl
tell return the position of a filehandle within a file
tie associate a variable with a database
time return number of seconds since January 1, 1970
tr/// replace characters in a string
truncate truncate a file (make it smaller)
uc uppercase a string
ucfirst uppercase first character of a string
umask change file creation mask
undef undefine (remove) a variable
unlink delete a file
unpack the reverse of pack
untie the reverse of tie
unshift move a value onto the beginning of an array
use import variables and functions from a library module
values return the values of a hash variable
wantarray return true in an array context
warn print a warning to standard error
write formatted report generation
Ok, now you know all the perl functions, so we're done. Thanks for coming.
16 of 20 Variables
A variable is a symbolic placeholder for a value, a lot like the variables in algebra. These values can be changed. Compare literals whose values cannot be changed. Perl has several built-in variable types:
Scalars: $variable_name A single-valued variable, always preceded by a $ sign.
Arrays: @array_name A multi-valued variable indexed by integer, preceded by an @ sign.
Hashes: %hash_name A multi-valued variable indexed by string, preceded by a % sign.
Filehandle: FILEHANDLE_NAME A file to read and/or write from. Filehandles have no special prefix, but are usually written in all uppercase.
We discuss arrays, hashes and filehandles later.
Scalar Variables
Scalar variables have names beginning with $. The name must begin with a letter or underscore, and can contain as many letters, numbers or underscores as you like. These are all valid scalars:
$foo $The_Big_Bad_Wolf $R2D2 $_____A23 $Once_Upon_a_Midnight_Dreary_While_I_Pondered_Weak_and_Weary
You assign values to a scalar variable using the = operator (not to be confused with ==, which is numeric comparison). You read from scalar variables by using them wherever a value would go.
A scalar variable can contain strings, floating point numbers, integers, and more esoteric things. You don't have to predeclare scalars. A scalar that once held a string can be reused to hold a number, and vice-versa:
Code:
$p = 'Potato'; # $p now holds the string "potato" $bushels = 3; # $bushels holds the value 3 $potatoes_per_bushel = 80; # $potatoes_per_bushel contains 80;
$total_potatoes = $bushels * $potatoes_per_bushel; # 240
print "I have $total_potatoes $p\n";
Output:
I have 240 Potato
Scalar Variable String Interpolation
The example above shows one of the interesting features of double-quoted strings. If you place a scalar variable inside a double quoted string, it will be interpolated into the string. With a single-quoted string, no interpolation occurs.
17 of 20 To prevent interpolation, place a backslash in front of the variable:
print "I have \$total_potatoes \$p\n";
# prints: I have $total_potatoes $p
Operations on Scalar Variables
You can use a scalar in any string or numeric expression like $hypotenuse = sqrt($x**2 + $y**2) or $name = $first_name . ' ' . $last_name. There are also numerous shortcuts that combine an operation with an assignment:
$a++ Increment $a by one
$a-- Decrement $a by one
$a += $b Modify $a by adding $b to it.
$a -= $b Modify $a by subtracting $b from it.
$a *= $b Modify $a by multiplying $b to it.
$a /= $b Modify $a by dividing it by $b.
$a .= $b Modify the string in $a by appending $b to it.
Example Code:
$potatoes_per_bushel = 80; # $potatoes_per_bushel contains 80;
$p = 'one'; $p .= ' '; # append a space $p .= 'potato'; # append "potato"
$bushels = 3; $bushels *= $potatoes_per_bushel; # multiply
print "From $p come $bushels.\n";
Output:
From one potato come 240.
String Functions that Come in Handy for Dealing with Sequences
Reverse the Contents of a String
18 of 20 $name = 'My name is Lincoln'; $reversed_name = reverse $name; print $reversed_name,"\n"; # prints "nlocniL si eman yM"
Translating one set of letters into another set
$name = 'My name is Lincoln'; # swap a->g and c->t $name =~ tr/ac/gt/; print $name,"\n"; # prints "My ngme is Lintoln"
Can you see how a combination of these two operators might be useful for computing the reverse complement?
Processing Command Line Arguments
When a Perl script is run, its command-line arguments (if any) are stored in an automatic array called @ARGV. You'll learn how to manipulate this array later. For now, just know that you can call the shift function repeatedly from the main part of the script to retrieve the command line arguments one by one.
Printing the Command Line Argument
Code:
#!/usr/bin/perl # file: echo.pl use strict; use warnings; $argument = shift; print "The first argument was $argument.\n";
Output:
(~) 50% chmod +x echo.pl (~) 51% echo.pl tuna The first argument was tuna. (~) 52% echo.pl tuna fish The first argument was tuna. (~) 53% echo.pl 'tuna fish' The first argument was tuna fish. (~) 53% echo.pl The first argument was.
Computing the Hypotenuse of a Right Triangle
19 of 20 Code:
#!/usr/bin/perl # file: hypotense.pl use strict; use warnings; $x = shift; $y = shift; $x>0 and $y>0 or die "Must provide two positive numbers";
print "Hypotenuse=",sqrt($x**2+$y**2),"\n";
Output:
(~) 82% hypotenuse.pl Must provide two positive numbers at hypotenuse.pl line 6. (~) 83% hypotenuse.pl 1 Must provide two positive numbers at hypotenuse.pl line 6. (~) 84% hypotenuse.pl 3 4 Hypotenuse=5 (~) 85% hypotenuse.pl 20 18 Hypotenuse=26.9072480941474 (~) 86% hypotenuse.pl -20 18 Must provide two positive numbers at hypotenuse.pl line 6.
20 of 20